Re: AMBER: average struct.problem

From: Thomas Cheatham <>
Date: Thu, 22 Jun 2006 08:35:45 -0600 (Mountain Standard Time)

> i have simulated a 12mer DNA with water and ion. After dynamics i did
> imaging of the trajectory file and saved is as a new file. i hv given
> the script below.
> trajin at_traj.mdcrd
> trajout at_imgd.mdcrd
> center :1-24 mass origin
> image origin center
> center:1-5223 mass origin
> image origin center familiar
> go
> now when i calculate the average structure from this imaged trajectory,
> all water molecules and ion cluster around the center of DNA. I have
> gone through the previous mails on this issue but i am not get whether
> the problem can be fixed. someone kindly help me on this.

Where do you think the water and ions should be? Hint: based on the
diffusion coefficient for your given water model (in the range of 2-5
m*m/s x10**-9) how far will a given water molecule move during the course
of your simulation? Is this larger than the box size? Hint2: look at a
movie of the whole system coloring a single water differently and watch
it move. Does it stay in one place?

What you are seeing seems entirely consistent for a coordinate average
over all the atoms in the system.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Sun Jun 25 2006 - 06:07:12 PDT
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